Prepare for release 1.2.24

Author: Uthpala Herath

docs/_modules/mechelastic/calculate_elastic.html

@@ -184,6 +184,7 @@ <h1>Source code for mechelastic.calculate_elastic</h1><div class="highlight"><pr
     <span class="n">code</span><span class="o">=</span><span class="s2">&quot;vasp&quot;</span><span class="p">,</span>
     <span class="n">anaddbfile</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
     <span class="n">qe_outfile</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+    <span class="n">qe_infile</span><span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
     <span class="n">adjust_pressure</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
     <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
     <span class="n">outfile</span><span class="o">=</span><span class="s2">&quot;elastic_properties.txt&quot;</span><span class="p">,</span>
@@ -210,6 +211,8 @@ <h1>Source code for mechelastic.calculate_elastic</h1><div class="highlight"><pr
 <span class="sd">        Path to the DDB file (applicable only in abinit). The default is None.</span>
 <span class="sd">    qe_outfile : str, optional</span>
 <span class="sd">        Path to the Quantum Espresso output file. The default is None.</span>
+<span class="sd">    qe_infile : str, optional</span>
+<span class="sd">        Path to the Quantum Espresso input file. The default is None.</span>
 <span class="sd">    adjust_pressure : bool, optional</span>
 <span class="sd">        To adjust the cell pressure according to the output file. The default is True.</span>
 <span class="sd">    verbose : str, optional</span>
@@ -225,7 +228,7 @@ <h1>Source code for mechelastic.calculate_elastic</h1><div class="highlight"><pr
 
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="c1"># Check if infile is present</span>
-    <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">infile</span><span class="p">):</span>
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">infile</span><span class="p">)</span> <span class="ow">and</span> <span class="n">code</span> <span class="o">==</span> <span class="s2">&quot;vasp&quot;</span><span class="p">:</span>
         <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%s</span><span class="s2"> doesn&#39;t exist. Exiting.&quot;</span> <span class="o">%</span> <span class="n">infile</span><span class="p">)</span>
         <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
 
@@ -255,13 +258,13 @@ <h1>Source code for mechelastic.calculate_elastic</h1><div class="highlight"><pr
         <span class="n">lattice_constant</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">lattice_constant</span>
 
     <span class="k">elif</span> <span class="n">code</span> <span class="o">==</span> <span class="s2">&quot;qe_ElaStic&quot;</span><span class="p">:</span>
-        <span class="n">output</span> <span class="o">=</span> <span class="n">QE_ElaStic_Parser</span><span class="p">(</span><span class="n">outfile</span><span class="o">=</span><span class="n">qe_outfile</span><span class="p">,</span> <span class="n">infile</span><span class="o">=</span><span class="n">infile</span><span class="p">)</span>
+        <span class="n">output</span> <span class="o">=</span> <span class="n">QE_ElaStic_Parser</span><span class="p">(</span><span class="n">outfile</span><span class="o">=</span><span class="n">qe_outfile</span><span class="p">,</span> <span class="n">infile</span><span class="o">=</span><span class="n">qe_infile</span><span class="p">)</span>
         <span class="n">elastic_tensor</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">elastic_tensor</span>
         <span class="n">structure</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">structure</span>
         <span class="n">lattice_constant</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">lattice_constant</span>
 
     <span class="k">elif</span> <span class="n">code</span> <span class="o">==</span> <span class="s2">&quot;qe_thermo_pw&quot;</span><span class="p">:</span>
-        <span class="n">output</span> <span class="o">=</span> <span class="n">QE_thermo_pw_Parser</span><span class="p">(</span><span class="n">outfile</span><span class="o">=</span><span class="n">qe_outfile</span><span class="p">,</span> <span class="n">infile</span><span class="o">=</span><span class="n">infile</span><span class="p">)</span>
+        <span class="n">output</span> <span class="o">=</span> <span class="n">QE_thermo_pw_Parser</span><span class="p">(</span><span class="n">outfile</span><span class="o">=</span><span class="n">qe_outfile</span><span class="p">,</span> <span class="n">infile</span><span class="o">=</span><span class="n">qe_infile</span><span class="p">)</span>
         <span class="n">elastic_tensor</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">elastic_tensor</span>
         <span class="n">structure</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">structure</span>
         <span class="n">lattice_constant</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">lattice_constant</span>

docs/_modules/mechelastic/parsers/abinitparser.html

@@ -331,7 +331,7 @@ <h1>Source code for mechelastic.parsers.abinitparser</h1><div class="highlight">
 
         <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">Printing Cij matrix as read from Abinit DDB output.</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
         <span class="n">np</span><span class="o">.</span><span class="n">set_printoptions</span><span class="p">(</span><span class="n">precision</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span> <span class="n">suppress</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-        <span class="n">printer</span><span class="o">.</span><span class="n">printMatrix</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+        <span class="n">printer</span><span class="o">.</span><span class="n">print_matrix</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">elastic_tensor</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
 
@@ -346,7 +346,7 @@ <h1>Source code for mechelastic.parsers.abinitparser</h1><div class="highlight">
 
         <span class="n">np</span><span class="o">.</span><span class="n">set_printoptions</span><span class="p">(</span><span class="n">precision</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="n">suppress</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 
-        <span class="n">printer</span><span class="o">.</span><span class="n">printMatrix</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">elastic_tensor</span><span class="p">)</span>
+        <span class="n">printer</span><span class="o">.</span><span class="n">print_matrix</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">elastic_tensor</span><span class="p">)</span>
 
         <span class="nb">print</span><span class="p">(</span>
             <span class="p">(</span>

docs/mechelastic.html

@@ -242,7 +242,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <span id="mechelastic-calculate-elastic-module"></span><h2>mechelastic.calculate_elastic module<a class="headerlink" href="#module-mechelastic.calculate_elastic" title="Permalink to this headline">¶</a></h2>
 <dl class="py function">
 <dt class="sig sig-object py" id="mechelastic.calculate_elastic.calculate_elastic">
-<span class="sig-prename descclassname"><span class="pre">mechelastic.calculate_elastic.</span></span><span class="sig-name descname"><span class="pre">calculate_elastic</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">infile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'OUTCAR'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'3D'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">elastic_tensor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">crystal</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lattice_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">code</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'vasp'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">anaddbfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">qe_outfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjust_pressure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'elastic_properties.txt'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/mechelastic/calculate_elastic.html#calculate_elastic"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mechelastic.calculate_elastic.calculate_elastic" title="Permalink to this definition">¶</a></dt>
+<span class="sig-prename descclassname"><span class="pre">mechelastic.calculate_elastic.</span></span><span class="sig-name descname"><span class="pre">calculate_elastic</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">infile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'OUTCAR'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'3D'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">elastic_tensor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">crystal</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lattice_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">code</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'vasp'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">anaddbfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">qe_outfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">qe_infile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjust_pressure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'elastic_properties.txt'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/mechelastic/calculate_elastic.html#calculate_elastic"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mechelastic.calculate_elastic.calculate_elastic" title="Permalink to this definition">¶</a></dt>
 <dd><p>Calculate the elastic properties of a material from a DFT calculation.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
@@ -264,6 +264,8 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 </dd>
 <dt><strong>qe_outfile</strong><span class="classifier">str, optional</span></dt><dd><p>Path to the Quantum Espresso output file. The default is None.</p>
 </dd>
+<dt><strong>qe_infile</strong><span class="classifier">str, optional</span></dt><dd><p>Path to the Quantum Espresso input file. The default is None.</p>
+</dd>
 <dt><strong>adjust_pressure</strong><span class="classifier">bool, optional</span></dt><dd><p>To adjust the cell pressure according to the output file. The default is True.</p>
 </dd>
 <dt><strong>verbose</strong><span class="classifier">str, optional</span></dt><dd><p>To print the progress of the elastic calculations. The default is True.</p>